Transcript Mutants - UBC Blogs

Lecture 2: Using Mutants to study
Biological processes
Objectives:
1. Why use mutants?
2. How are mutants isolated?
3. What important genetic analyses must be done
immediately after a genetic screen for mutants?
Reading
• References:
• Cove. 1993. Mutant analysis, a key tool for the
study of metabolism and development. Plant
Journal 3: 303-308.
• Westhoff et. al. Molecular Plant Development:
from gene to plant. Chapter 3: 39-65.
Information obtained from sequencing the
Arabidopsis genome
Genome size:
115 Mbp sequenced +
10 Mbp highly repetitive: (rDNA,
Centromere)
= 125 Mbp
Sequence is 99.99% accurate
Annotation
Identification of genes:
How? Use known sequence features of genes to predict:
Open reading frames, Splice junctions, promoter elements,
base composition, translation initiation sites.
Refine with cDNA sequence.
Predict:
(estimates)
Arabidopsis
C. elegans
D. melanogaster
27,000
19,000
14,000
Gene function
Define gene function on the basis of
Biochemical role
Based on sequence similarity to known proteins
+ 900 non-coding
Plant Functional Genomics Chris Somerville* and Shauna Somerville. 1999 SCIENCE VOL 285
Biological process?
Cellular function?
Scope of the problem
• All genes in Arabidopsis have been identified through genome
sequencing so cloned genes are readily accessible.
But of 27,000 genes:
Known biochemical/ cellular/biological function
# genes
1,000
Predicted biochemical function from annotation 16,000
Unknown
10,000
Why use mutants?
Researchers need both phenotypic and biochemical (protein function)
information about their gene to understand its role.
The identification of a gene by mutant phenotype = forward genetics
-use phenotype to find associated DNA sequence
The identification of a gene by DNA sequence
-use sequence to find a mutant with a defect in
that gene
= reverse genetics
Forward genetics
Goal:
Identify genes with a role in a specific biological process
by finding mutants defective in that process.
Mutant phenotypes provide
-- information concerning the role of the gene in vivo.
-- method by which to clone the gene that is mutated.
Mutagenesis
1.
Mutants are generated by exposing a population of organisms to a
mutagen and allowing the individuals in the population to
reproduce.
mutagens = irradiation (UV, Xray, fast neutron, etc.), chemicals
(ethyl methane sulfonate, nitrosoguanidine etc.), insertional
elements (transposons, TDNA)
2.
The mutagen induces multiple mutations in the genome of the
cells exposed (M1 generation)
Mutagenesis in Arabidopsis
Mutagenized cells are heterozygous in diploids
Westhoff Fig. 3.1
Mutagenesis
1.
Mutants are generated by exposing a population of organisms to a
mutagen and allowing the individuals in the population to
reproduce.
mutagens = irradiation (UV, Xray, fast neutron, etc.), chemicals (ethyl
methane sulfonate, nitrosoguanidine etc.), insertional elements
(transposons, TDNA)
2.
The mutagen induces multiple mutations in the genome of the
cells exposed (M1 generation)
The M1 plants are not typically screened for mutant phenotypes-Why?
Mutagenesis
1.
Mutants are generated by exposing a population of organisms to a
mutagen and allowing the individuals in the population to
reproduce.
mutagens = irradiation (UV, Xray, fast neutron, etc.), chemicals (ethyl
methane sulfonate, nitrosoguanidine etc.), insertional elements
(transposons, TDNA)
2.
The mutagen induces multiple mutations in the genome of the
cells exposed (M1 generation; mutations are heterozygous in
diploids).
--Those mutations in germline cells are passed on to the next
generation (M2 generation).
--In plant species that self fertilize (eg. Arabidopsis) the M2
population will include some plants homozygous for mutations.
Therefore: The M2 generation is typically screened for mutant
phenotypes
Mutagenesis in Arabidopsis
Westhoff Fig. 3.1
Genetic Nomenclature (Arabidopsis, yeast)
A gene is typically named after the mutant phenotype or the
biological function with which it was identified.
Mutant phenotype =
George or george (italics)
Gene name
(abbreviation)
GEORGE (uppercase, italics)
GEO
=
=
geo-1 (lowercase italics)
geo-2
geo-3
dominance/recessiveness is not indicated
protein
=
GEO (uppercase, no italics)
mutant alleles
=
Basic Genetic Analysis of Mutants
(what you should know genetically about any mutant you find)
You screened a large mutagenized (M2) population and found three
plants with curled leaves, sepals and petals .
Hypothesis: Each plant is homozygous for a recessive allele of a single
nuclear gene that is needed for the leafy organs of the plant to
develop normally.
Phenotype = Curly Leaf (Crl) Gene = CRL alleles = crl-1, crl-2, crl-3
How do you test your hypothesis?
What are the competing hypotheses?
Basic Genetic Analysis of Mutants
1.
Is the mutant phenotype heritable?
Allow the plant to self fertilize. Does the phenotype show
up in the next generation?
Yes
heritable
No phenotype is probably not due to mutation.
Basic Genetic Analysis of Mutants
2.
Is the mutant phenotype due to a recessive,
codominant or dominant mutant allele?
Cross the mutant plant to wild type. If the F1 progeny
phenotype is:
i) wild type then the mutant allele is recessive (most
common)
ii) mutant then the mutant allele is dominant
iii) intermediate between wild type and mutant then the
mutant allele is co-dominant.
Basic Genetic Analysis of Mutants
3.
Is the phenotype of a each mutant due to mutation of one or more
than one nuclear genes?
Self fertilize the F1 plants and determine the number and type of mutant
phenotypes among the F2 progeny.
¾ wild type, ¼ curly leaves,petals,sepals (mutant allele recessive) or
¾ curly leaves,petals,sepals , ¼ wild type (mutant allele dominant)
=
single nuclear mutation
9/16 wild type, 3/16 curly leaves(normal petals and sepals), 3/16 curly
sepals and petals (normal leaves), 1/16 curly leaves, petals, sepals
= two nuclear genes, one required for normal leaf development and
another required for normal floral organ development.
Basic Genetic Analysis of Mutants
(Co)Segregation analysis:
If two aspects of a phenotype (eg. Curly and white leaves)
segregate together (if all plants with curly leaves also
have white leaves and vice versa) an F2 population then
the mutation(s) causing the phenotypes are closely
linked and may be caused by a single mutation.
If two aspects of a phenotype can be observed separately in
an F2 population (plants with only curly or white leaves)
then they are not caused by the same mutation and are
due to mutations in at least two different genes (a single
recombinant would indicate that two traits are not due to
the same mutation).
Basic Genetic Analysis of Mutants
Three Crl mutants were found. Do they represent mutations
in three different genes or three alleles of the same
gene?
If the mutants are recessive to wild type and the phenotype
segregate as a single nuclear gene then the question
can be answered by a:
Complementation test
Complementation test
The idea of a complementation test is that for a
mutant that is homozygous for a recessive (loss-of
function) mutation that results in a phenotype, the
phenotype can be rescued (complemented) if at least
one normal (wild type) copy of the gene is introduced.
A normal copy of the gene can be introduced by
crossing the mutant to a wild type plant (classical
complementation) or introducing a copy by
transformation.
Complementation test
Mutant 1
Crl
Mutant 2
Crl
Mutant 3
Crl
All mutants are recessive to wild type. All segregate as single nuclear
genes.
How many genes have been identified?
Test
Mutant1
Crl
x
Mutant 2
Crl
Possibilities: 1, 2, 3
Deduction
Mutant1
x
crl1-1/ crl1-1
Mutant 2
crl1-2/ crl1-2
Result
F1
Crl
F1
crl1-1/ crl1-2
Conclusion: Mutants 1 and 2 fail to complement and must be homozygous
for mutations in the same gene
Complementation test
Mutant 1
Crl
Test
x
Mutant 3
Crl
Deduction
Mutant1
x
Mutant 3
crl1-1/ crl 1-1
CRL 1/ CRL 1
CRL 2/ CRL 2
crl 2-1/ crl 2-1
Result
F1
Normal leaves, sepals,petals
Conclusion:
Mutants 1 and 3 are in different
complementation groups. Mutants
Are homozygous for mutant alleles
of different genes.
F1
crl-1/ CRL1
CRL2/ crl2-1
To have a wild type phenotype the F1
must be heterozygous for mutant
alleles of two different genes.
Conclusion: The three Crl mutants identify two different genes required for
normal leafy organs.
CRL1 and CRL2